| Next changeset 1:8c2e674a93bb (2020-04-07) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f" |
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added:
data_manager/kma_build_index.py data_manager/kma_build_index.xml data_manager_conf.xml test-data/kma_data_manager.json test-data/phiX174.fasta tool-data/kma_index.loc.sample tool_data_table_conf.xml.sample |
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| diff -r 000000000000 -r 889cc43b72d6 data_manager/kma_build_index.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/kma_build_index.py Tue Feb 18 16:24:23 2020 -0500 |
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| @@ -0,0 +1,96 @@ +#!/usr/bin/env python + +from __future__ import print_function + +import argparse +import errno +import json +import os +import subprocess +import uuid + + +DATA_TABLE_NAME = "kma_index" + + +def kma_build_index(kma_index_args, index_name, target_directory, data_table_name=DATA_TABLE_NAME): + UUID = str(uuid.uuid4()) + + os.mkdir(os.path.join(target_directory, UUID)) + + args = [ + '-k', str(kma_index_args["k"]), + '-k_t', str(kma_index_args["k_t"]), + '-k_i', str(kma_index_args["k_i"]), + '-ML', str(kma_index_args["ML"]), + '-ht', str(kma_index_args["ht"]), + '-hq', str(kma_index_args["hq"]), + '-o', os.path.join(UUID, "index"), + '-i', " ".join(kma_index_args["fasta"]), + ] + + subprocess.check_call(' '.join(['kma index'] + args), cwd=target_directory, shell=True) + + data_table_entry = { + 'data_tables': { + data_table_name: [ + { + "value": UUID, + "name": index_name, + "path": os.path.join(UUID, "index"), + } + ] + } + } + + return data_table_entry + + +def main(args): + + data_manager_input = json.loads(open(args.data_manager_json).read()) + + target_directory = data_manager_input['output_data'][0]['extra_files_path'] + + try: + os.mkdir( target_directory ) + except OSError as exc: + if exc.errno == errno.EEXIST and os.path.isdir( target_directory ): + pass + else: + raise + + data_manager_output = {} + + kma_index_args = { + "k": args.k, + "k_t": args.k_t, + "k_i": args.k_i, + "ML": args.ML, + "ht": args.ht, + "hq": args.hq, + "fasta": args.fasta, + } + + data_manager_output = kma_build_index( + kma_index_args, + args.index_name, + target_directory, + ) + + open(args.data_manager_json, 'w').write(json.dumps(data_manager_output)) + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument('data_manager_json') + parser.add_argument('--k', dest='k', type=int, default=16, help='') + parser.add_argument('--k_t', dest='k_t', type=int, default=16, help='') + parser.add_argument('--k_i', dest='k_i', type=int, default=16, help='') + parser.add_argument('--ML', dest='ML', type=int, default=16, help='') + parser.add_argument('--ht', dest='ht', type=float, default=1.0, help='') + parser.add_argument('--hq', dest='hq', type=float, default=1.0, help='') + parser.add_argument('--name', dest='index_name', help='') + parser.add_argument('fasta', nargs='+', help='fasta file(s) to index') + args = parser.parse_args() + main(args) |
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| diff -r 000000000000 -r 889cc43b72d6 data_manager/kma_build_index.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/kma_build_index.xml Tue Feb 18 16:24:23 2020 -0500 |
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| @@ -0,0 +1,48 @@ +<?xml version="1.0"?> +<tool id="kma_build_index" name="KMA Index Builder" tool_type="manage_data" version="1.2.21+galaxy0" profile="19.01"> + <description>kma index builder</description> + <requirements> + <requirement type="package" version="1.2.21">kma</requirement> + <requirement type="package" version="3.7">python</requirement> + </requirements> + <version_command>kma -v</version_command> + <command detect_errors="exit_code"> + <![CDATA[ + python '${__tool_directory__}/kma_build_index.py' + '${out_file}' + --k ${k} + --k_t ${k_t} + --k_i ${k_i} + --ML ${ML} + --ht ${ht} + --hq ${hq} + --name '${name}' + '${fasta}' + ]]> + </command> + <inputs> + <param name="k" type="integer" value="16" min="8" max="32" label="kmer size used for indexing the database." /> + <param name="k_t" type="integer" value="16" min="8" max="32" label="kmer size used to identify template candidates when running KMA." /> + <param name="k_i" type="integer" value="16" min="8" max="32" label="kmer size used when performing alignments between two sequences." /> + <param name="ML" type="integer" value="16" label="Minimum length of templates" /> + <param name="ht" type="float" value="1.0" min="0.0" max="1.0" label="Homology template" /> + <param name="hq" type="float" value="1.0" min="0.0" max="1.0" label="Homology query" /> + <param name="name" type="text" label="Name for index" /> + <param name="fasta" type="data" format="fasta" label="Sequence to index (fasta)" /> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json" /> + </outputs> + <tests> + <test> + <param name="fasta" value="phiX174.fasta"/> + <param name="name" value="index"/> + <output name="out_file" value="kma_data_manager.json" compare="sim_size" /> + </test> + </tests> + <help> + </help> + <citations> + <citation type="doi">10.1186/s12859-018-2336-6</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 889cc43b72d6 data_manager_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Tue Feb 18 16:24:23 2020 -0500 |
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| @@ -0,0 +1,18 @@ +<data_managers> + <data_manager tool_file="data_manager/kma_build_index.xml" id="kma_build_index" version="0.1.0"> + <data_table name="kma_index"> + <output> + <column name="value"/> + <column name="name"/> + <column name="path" output_ref="out_file"> + <move type="directory"> + <source>#import os#${os.path.dirname($path)}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kma_index/#import os#${os.path.dirname($path)}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/kma_index/${path}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + </data_manager> +</data_managers> |
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| diff -r 000000000000 -r 889cc43b72d6 test-data/kma_data_manager.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kma_data_manager.json Tue Feb 18 16:24:23 2020 -0500 |
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| @@ -0,0 +1,1 @@ +{"data_tables": {"kma_index": [{"name": "b153d490-f0f2-4980-8d1b-c7365e4d69ec/index", "path": "index", "value": "b153d490-f0f2-4980-8d1b-c7365e4d69ec"}]}} |
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| diff -r 000000000000 -r 889cc43b72d6 test-data/phiX174.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiX174.fasta Tue Feb 18 16:24:23 2020 -0500 |
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| @@ -0,0 +1,79 @@ +>phiX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT +GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA +ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG +TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA +GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC +TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT +TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT +CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT +TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG +TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC +GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA +CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG +TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT +AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC +CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA +TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC +TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA +CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA +GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT +GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA +ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC +TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT +TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC +ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC +CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT +GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC +CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC +TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG +TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT +TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA +AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT +TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT +ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC +GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC +TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT +TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA +TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG +TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC +CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG +AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC +CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT +TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG +CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA +AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT +GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG +GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA +TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT +CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG +TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA +GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC +CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA +TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA +AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC +TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT +CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA +TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG +TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT +CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT +TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC +ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG +TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA +ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG +GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC +CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT +GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG +GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT +ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG +CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC +CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC +GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT +CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG +CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA +TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT +TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG +TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC +AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC +TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA + |
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| diff -r 000000000000 -r 889cc43b72d6 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Feb 18 16:24:23 2020 -0500 |
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| @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of kma indexes in the required format --> + <table name="kma_index" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/kma_index.loc" /> + </table> +</tables> |